Quantifying RNA Degradation with Single-Molecule Nanopore Sensing

RNA is the key biomolecule in innumerable diagnostic and therapeutic applications, but its chemical instability plagues researchers and clinicians alike. Gel electrophoresis remains the predominant method for the assessment of RNA degradation. The main drawback is the quantity of RNA required─typically 100 ng or more. To study the degradation profiles of mRNA vaccines, viral and bacterial RNA, and other valuable species, new sensitive and quantitative methodologies are required. We present the use of solid-state nanopore sensing to evaluate the degradation of viral RNA under various conditions with single-molecule resolution. While relying on similar principles to gel electrophoresis, nanopore sensing is suitable for use over a wide range of concentration regimes, with even 100 pg of RNA being sufficient for analysis. Our results demonstrate the utility of nanopore assays in assessing RNA integrity for samples not suitable for gel-based analyses due to low abundance or high molecular weight.